• Working @Epiforecasts (part of theLondon School of Hygiene and Tropical Medicine);
• ⭐ Contributing to theepinowcast community developing tools and methods for current surveillance of infectious disease and preparing for future outbreaks;
• 🧻 Currently working on:
  • If we want an estimate of the reproduction number do we need the renewal process? and associated Julia modelling toolkit.
  • Developing a workbench for real-time and outbreak infectious disease modelling
  • Course materials on nowcasting, forecasting, and evaluation
  • 😴 🔌 🐑

• 🏢 2024-: Assistant professor in real-time modelling of infectious disease w/Sebastian Funk at theLondon School of Hygiene and Tropical Medicine
• 🏢 2023-2025: Contractor supporting theUS CDC Centre for Forecast and Outbreak Analytics
• 🏢 2020-2023: Postdoc in real-time modelling of infectious disease w/Sebastian Funk at theLondon School of Hygiene and Tropical Medicine
• 🏢 2017-2019: Data Scientist atFunding Circle
• 📜 2016-2019:PhD at theUniversity of Bristol on modelling the use of the BCG vaccine in the UK
• ⚙️ I use daily:R,julia,stan
• 🏗️ I like to perform analysis using novel models on interesting data and generalise those approaches into software 📦s
• 🌍 I'm mostly active within theepinowcast community
• 🌱 Learning all aboutJulia andTuring.jl - currently wondering why in the world you would use callables.
• 📘 Reading:Probability and random processes
• 💬 Ping me aboutstatistical modelling of infectious diseases,real-time analysis of infectious diseases,estimating transmission dynamics in real-time, andteam science opportunities
• 📫 Reach me:contact@samabbott.co.ukprob

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1. thesisthesisPublic

   PhD thesis submitted to the University of Bristol. Title: Modelling BCG vaccination in the UK: What is the impact of changing policy?

   C++ 11 2

2. epiforecasts/EpiNow2epiforecasts/EpiNow2Public

   Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

   R 123 36

3. epiforecasts/covidregionaldataepiforecasts/covidregionaldataPublic

   An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisa…

   R 37 16

4. epiforecasts/forecast.vocsepiforecasts/forecast.vocsPublic

   Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluatio…

   R 8 3

5. epinowcast/epinowcastepinowcast/epinowcastPublic

   Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

   R 61 21

6. epiforecasts/scoringutilsepiforecasts/scoringutilsPublic

   Utilities for Scoring and Assessing Predictions

   R 52 23